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- PDB-5xxs: Crystal structure of native ribT from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 5xxs
TitleCrystal structure of native ribT from Bacillus subtilis
ComponentsProtein RibT
KeywordsTRANSFERASE / Riboflavin / CoA / GNAT / acetylation
Function / homologyriboflavin biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Acyl-CoA N-acyltransferase / COENZYME A / Protein RibT
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsSrivastava, R. / Karthikeyan, S.
Funding support India, 1items
OrganizationGrant numberCountry
CSIRBSC 0104 India
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Structural characterization of ribT from Bacillus subtilis reveals it as a GCN5-related N-acetyltransferase.
Authors: Srivastava, R. / Kaur, A. / Sharma, C. / Karthikeyan, S.
History
DepositionJul 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein RibT
B: Protein RibT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2589
Polymers31,3312
Non-polymers1,9267
Water1,60389
1
A: Protein RibT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6405
Polymers15,6661
Non-polymers9754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-2 kcal/mol
Surface area6720 Å2
MethodPISA
2
B: Protein RibT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6174
Polymers15,6661
Non-polymers9523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-0 kcal/mol
Surface area7420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.580, 57.444, 74.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein RibT


Mass: 15665.743 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ribT, BSU23240 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P17622, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.32 % / Description: Two dimensional Plate like
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 80% 2.7M sodium malonate, 20% 2.1M Malic acid / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 27, 2015 / Details: Mirror
RadiationMonochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 13197 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / CC1/2: 0.94 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.7
Reflection shellResolution: 2.08→2.12 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 395 / CC1/2: 0.74 / % possible all: 56.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XXR

5xxr


Resolution: 2.09→34.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.533 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.25 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26691 1308 9.9 %RANDOM
Rwork0.19974 ---
obs0.20662 11888 92.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.667 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å2-0 Å2-0 Å2
2---2.19 Å20 Å2
3---3.8 Å2
Refinement stepCycle: 1 / Resolution: 2.09→34.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 121 89 2102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192043
X-RAY DIFFRACTIONr_bond_other_d0.0010.021843
X-RAY DIFFRACTIONr_angle_refined_deg1.3382.022757
X-RAY DIFFRACTIONr_angle_other_deg0.90334279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.035238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38725.16193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25515358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7841510
X-RAY DIFFRACTIONr_chiral_restr0.0710.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9764.03958
X-RAY DIFFRACTIONr_mcbond_other1.9664.029957
X-RAY DIFFRACTIONr_mcangle_it3.1596.0371194
X-RAY DIFFRACTIONr_mcangle_other3.1636.0391195
X-RAY DIFFRACTIONr_scbond_it2.0964.2231085
X-RAY DIFFRACTIONr_scbond_other2.0934.2231085
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4666.2311564
X-RAY DIFFRACTIONr_long_range_B_refined5.51946.1812153
X-RAY DIFFRACTIONr_long_range_B_other5.48446.0612144
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.095→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 52 -
Rwork0.249 505 -
obs--54.03 %

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